# hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: pfam_list/SpoU_methylase.hmm.txt # target sequence database: proteomes/Pseudomonas_aeruginosa.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoU_methylase [M=142] Accession: PF00588.18 Description: SpoU rRNA Methylase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-41 137.8 0.0 1.1e-40 137.4 0.0 1.2 1 sp|Q9HUM8|RLMB_PSEAE 23S rRNA (guanosine-2'-O-)-methyltran 3.2e-34 116.5 0.0 4.9e-34 115.9 0.0 1.3 1 tr|Q9HXI5|Q9HXI5_PSEAE tRNA (cytidine/uridine-2'-O-)-methylt 4.5e-32 109.5 0.0 5.1e-32 109.4 0.0 1.0 1 tr|Q9HU57|Q9HU57_PSEAE tRNA (cytidine(34)-2'-O)-methyltransf ------ inclusion threshold ------ 0.042 12.4 0.2 0.049 12.1 0.2 1.2 1 tr|Q9HZU6|Q9HZU6_PSEAE Uncharacterized protein OS=Pseudomona Domain annotation for each sequence (and alignments): >> sp|Q9HUM8|RLMB_PSEAE 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB OS=Pseudomonas aeruginosa (strain ATCC 15692 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 137.4 0.0 7.9e-44 1.1e-40 2 142 .] 98 238 .. 97 238 .. 0.97 Alignments for each domain: == domain 1 score: 137.4 bits; conditional E-value: 7.9e-44 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEEST.T-SEGC CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatsl.kgksls 89 l ++l++++dp+NlGa++Rta+a+g++++++ k++sa +ln +++++a+ga+ev++l+ v++l+++l++l+++g+++v+t + +k+l+ sp|Q9HUM8|RLMB_PSEAE 98 LLLALDGVTDPHNLGACLRTADAAGVQAVIVPKDKSA-TLNATVRKVACGAAEVIPLVAVTNLARTLEKLQQRGLWVVGTAGeADKTLY 185 6799***************************998887.9*******************************************8999999 PP CSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS SpoU_methylase 90 eidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142 ++dlk++++lv+G E+kG+++ ++e++d l ++pm+g+v+SLNv+vA++++l+ sp|Q9HUM8|RLMB_PSEAE 186 QLDLKGPTVLVMGAEGKGMRRLTREHCDFLARLPMAGSVSSLNVSVATGVCLF 238 **************************************************985 PP >> tr|Q9HXI5|Q9HXI5_PSEAE tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ OS=Pseudomonas aeruginosa (strain ATCC 1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 115.9 0.0 3.5e-37 4.9e-34 2 142 .] 5 155 .. 4 155 .. 0.87 Alignments for each domain: == domain 1 score: 115.9 bits; conditional E-value: 3.5e-37 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEEEEEESTT-SE CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfalvatslkgks 87 ++vvlv++++pgN+G +aR++k++g+s+lvlv+p+s+ + +a++ a+ga ++l+ ++vvd+leeal + + ++ts+++++ tr|Q9HXI5|Q9HXI5_PSEAE 5 IRVVLVNTSHPGNIGGAARAMKNMGLSQLVLVQPESF--PHGDAVARASGATDILDaARVVDTLEEALIGCSVV----LGTSARDRR 85 79**********************************9..6666777779*******9999***********998....999998887 PP GC....CS...........HHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS SpoU_methylase 88 ls....ei...........dlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142 + + + +++valvfG+E +Gl+ne+l++++ +v+Ip ++e+ SLN+a Av++l y tr|Q9HXI5|Q9HXI5_PSEAE 86 IPwpllDPrecattclehlEANGEVALVFGREYAGLTNEELQRCQFHVHIPSDPEFGSLNLAAAVQVLTY 155 7765552244444444444555*********************************************987 PP >> tr|Q9HU57|Q9HU57_PSEAE tRNA (cytidine(34)-2'-O)-methyltransferase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 109.4 0.0 3.6e-35 5.1e-32 2 142 .] 2 142 .. 1 142 [. 0.95 Alignments for each domain: == domain 1 score: 109.4 bits; conditional E-value: 3.6e-35 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEEST.T-SE CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatsl.kgks 87 ++v+l+++e+p N+G+i+R+++++g+ l+l++p +++l++++++ra+++++e+ +++++ l+++l++l + +l+a+++ +++ tr|Q9HU57|Q9HU57_PSEAE 2 FHVILFQPEIPPNTGNIIRLCANAGC-SLHLIEPLGFELDDKRLRRAGLDYHEYASVRRYPYLQSCLEALGQP--RLFAFTTkGSRA 85 78************************.9*******************************************99..888888857888 PP GCCSHHHTTEEEEEEBTTTBS-HHHHCTSS..EEEE----TTSSS--HHHHHHHHHH CS SpoU_methylase 88 lseidlkekvalvfGnEdkGlsnellelad..rlvkIpmsgeveSLNvavAvailly 142 ++e+++++ a++fG+E++Gl++++++++ r +++pm++ +SLN++++va+ +y tr|Q9HU57|Q9HU57_PSEAE 86 FHEVAYQRGDAFLFGPESRGLPEDVRNALPtdRRLRLPMREGCRSLNLSNTVAVTVY 142 89************************9975559*********************987 PP >> tr|Q9HZU6|Q9HZU6_PSEAE Uncharacterized protein OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 12.1 0.2 3.5e-05 0.049 19 91 .. 3 74 .. 1 95 [. 0.75 Alignments for each domain: == domain 1 score: 12.1 bits; conditional E-value: 3.5e-05 HHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGCCS CS SpoU_methylase 19 aRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgkslsei 91 +R + a+g+ +l l++ s+d+ e +r++ +ale+ +++ +++ + lk +++ +a + ++s++++ tr|Q9HZU6|Q9HZU6_PSEAE 3 IRWMMAAGLAALTLSGCASNDPAPLEQMRLTEQALEQAKAVGATDDVAELKLAQDK-YAAAQIAMTAESYKKA 74 8**************************************55544444446666666.5555554466666655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (142 nodes) Target sequences: 5563 (1857172 residues searched) Passed MSV filter: 126 (0.0226496); expected 111.3 (0.02) Passed bias filter: 107 (0.0192342); expected 111.3 (0.02) Passed Vit filter: 12 (0.00215711); expected 5.6 (0.001) Passed Fwd filter: 4 (0.000719036); expected 0.1 (1e-05) Initial search space (Z): 5563 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 26371.84 // [ok]